Multiple platform build/check report for BioC 3.8 - CHECK report for geneClassifiers on tokay1

Package: geneClassifiers

Version: 1.6.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:geneClassifiers.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings geneClassifiers_1.6.0.tar.gz

StartedAt: 2019-04-13 02:27:33 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 02:29:22 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 109.3 seconds

RetCode: 0

Status: OK

CheckDir: geneClassifiers.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:geneClassifiers.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings geneClassifiers_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/geneClassifiers.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'geneClassifiers/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'geneClassifiers' version '1.6.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'geneClassifiers' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/geneClassifiers_1.6.0.tar.gz && rm -rf geneClassifiers.buildbin-libdir && mkdir geneClassifiers.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=geneClassifiers.buildbin-libdir geneClassifiers_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL geneClassifiers_1.6.0.zip && rm geneClassifiers_1.6.0.tar.gz geneClassifiers_1.6.0.zip
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1278k  100 1278k    0     0  24.3M      0 --:--:-- --:--:-- --:--:-- 26.0M

install for i386

* installing *source* package 'geneClassifiers' ...
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'geneClassifiers'
    finding HTML links ... done
    ClassifierParameters                    html  
    ClassifierResults                       html  
    FixedExpressionData                     html  
    bracket-methods                         html  
    dim-methods                             html  
    exampleMAS5                             html  
    finding level-2 HTML links ... done

    getBatchCorrection-methods              html  
    getCitations-methods                    html  
    getClassifications-methods              html  
    getClassifier-methods                   html  
    getDecisionBoundaries-methods           html  
    getDescription-methods                  html  
    getEventChain-methods                   html  
    getIntercept-methods                    html  
    getMeans-methods                        html  
    getName-methods                         html  
    getNormalizationMethod-methods          html  
    getProbeNames-methods                   html  
    getScores-methods                       html  
    getSds-methods                          html  
    getTargetValue-methods                  html  
    getTrainingData-methods                 html  
    getWeightingType-methods                html  
    getWeights-methods                      html  
    runClassifier-methods                   html  
    setNormalizationMethod-methods          html  
    showClassifierList-methods              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'geneClassifiers' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'geneClassifiers' as geneClassifiers_1.6.0.zip
* DONE (geneClassifiers)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'geneClassifiers' successfully unpacked and MD5 sums checked
In R CMD INSTALL


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(geneClassifiers)
> 
> test_check("geneClassifiers")
== testthat results  ===========================================================
OK: 136 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   1.51    0.07    1.57


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(geneClassifiers)
> 
> test_check("geneClassifiers")
== testthat results  ===========================================================
OK: 136 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   2.51    0.06    2.62

name	user	system	elapsed
bracket-methods	0.04	0.01	0.06
dim-methods	0.03	0.00	0.03
getBatchCorrection-methods	0.22	0.02	0.23
getCitations-methods	0	0	0
getClassifications-methods	0.04	0.00	0.05
getClassifier-methods	0	0	0
getDecisionBoundaries-methods	0	0	0
getDescription-methods	0	0	0
getEventChain-methods	0	0	0
getIntercept-methods	0	0	0
getMeans-methods	0	0	0
getName-methods	0	0	0
getNormalizationMethod-methods	0.05	0.03	0.08
getProbeNames-methods	0	0	0
getScores-methods	0.05	0.02	0.06
getSds-methods	0	0	0
getTargetValue-methods	0.01	0.02	0.03
getTrainingData-methods	0.04	0.00	0.03
getWeightingType-methods	0.01	0.03	0.05
getWeights-methods	0	0	0
runClassifier-methods	0.06	0.00	0.06
setNormalizationMethod-methods	0.05	0.00	0.05
showClassifierList-methods	0.05	0.00	0.04

name	user	system	elapsed
bracket-methods	0.05	0.00	0.04
dim-methods	0.01	0.01	0.04
getBatchCorrection-methods	0.27	0.00	0.26
getCitations-methods	0	0	0
getClassifications-methods	0.04	0.00	0.05
getClassifier-methods	0	0	0
getDecisionBoundaries-methods	0	0	0
getDescription-methods	0	0	0
getEventChain-methods	0	0	0
getIntercept-methods	0.02	0.00	0.01
getMeans-methods	0	0	0
getName-methods	0	0	0
getNormalizationMethod-methods	0.06	0.00	0.07
getProbeNames-methods	0	0	0
getScores-methods	0.05	0.02	0.06
getSds-methods	0	0	0
getTargetValue-methods	0.02	0.00	0.01
getTrainingData-methods	0.04	0.00	0.05
getWeightingType-methods	0.03	0.00	0.03
getWeights-methods	0.02	0.00	0.02
runClassifier-methods	0.05	0.00	0.05
setNormalizationMethod-methods	0.03	0.00	0.03
showClassifierList-methods	0.04	0.00	0.04

CHECK report for geneClassifiers on tokay1

Summary

Command output

Installation output

Tests output

Example timings